Despite the existence of many electronic bill payment systems, many banks, credit card companies, utilities, businesses, and other institutions that bill customers still receive a substantial amount of payments in the mail. Opening, sorting, and processing all of this mail can be costly and time consuming. Furthermore, paper-based communication also allows for a significant amount of exception situations that further complicate the payment receiving process. For example, some customers may send a check alone, other customers may send the invoice with the check, and still others may send a check with some other piece of paper containing instructions or other communications for the institution. An automated system for processing paper-based payments and appropriately handling exception situations would be desirable.